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The council voted to approve its submission on the Government plans to merge the country's 16 polytechnics into a single national institute.
The submission supports Mr Ker's alternative plan, which would allow polytechnics to keep control of their decision-making and budgets.
Mayor Dave Cull said Otago polytechnic was not only one of the best in New Zealand in terms of education and community involvement, it had also remained commercially viable, despite a difficult funding environment.
Taking local control away from successful polytechnics would only result in a ''dumbing down'' of the sector which is the opposite of what the Government was trying to achieve, Mr Cull said.
''We could end up with a complete collapse so we need our polytech to remain at least semi-autonomous so it can be an exemplar for the rest of the country like it has been for the past few years.''
Cr Andrew Whiley urged others make a submission in support of the polytechnic before the April 5 deadline.
After voting to approve the submission, councillors also officially thanked Mr Ker and the rest of the staff at the polytechnic for their work.
A motion was put for the council to record a vote of thanks to Mr Ker and the rest of the staff for their stewardship of the institution and for their constructive engagement with the proposals to improve the polytechnic sector across the country.
Councillors voted unanimously to support both the submission and the vote of thanks.